Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005065.1 Corchorus capsularis cultivar CVL-1 contig05083, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9562
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:461 original size:154 final size:150
Alignment explanation
Indices: 165--496 Score: 470
Period size: 154 Copynumber: 2.2 Consensus size: 150
155 TCATAATTTG
* * *
165 AATAAAACTAATGTTCATTTTATAATTAGTTAGCAACATTCTTAGAAATGAAATATAATTTCGTA
1 AATAAAACTAATTTTCATTTTATAATTAGCTAGCAACATTCTTAGAAATGAAATATAATTCCGTA
*
230 TGAAATTCCGTTTCTAAGTGAAACATTTATAGATGAAATTATTTCTGTAAATATTTCCACTCCTT
66 TGAAATTCCGTTTCTAAGTGAAAAATTTATAGATGAAATTATTTCTGTAAATATTTCCACTCCTT
*
295 ATCTTTATAATAAT-AATCTA
131 ATCTTTATAATAATCAA-ATA
* *
315 AATAAAACTAATTTTCATTTGATAATTAGCTAGCAACGTTCTTAGAAATGGAAATATAATTGCCG
1 AATAAAACTAATTTTCATTTTATAATTAGCTAGCAACATTCTTAGAAAT-GAAATATAATT-CCG
* *
380 TGTGAAATTCCGTTTCCT-AGTGAAAAAAATTTATAGATGAAATTATTTCTTTAAATATTTCCAC
64 TATGAAATTCCGTTT-CTAAGTG--AAAAATTTATAGATGAAATTATTTCTGTAAATATTTCCAC
* *
444 TTCTTGTCTTTATAATAATCCAAATA
126 TCCTTATCTTTATAATAAT-CAAATA
* *
470 TATAAAATTAATTTTCATTTTATAATT
1 AATAAAACTAATTTTCATTTTATAATT
497 TTTTTTGGCA
Statistics
Matches: 161, Mismatches: 14, Indels: 9
0.88 0.08 0.05
Matches are distributed among these distances:
150 45 0.28
151 11 0.07
152 20 0.12
153 2 0.01
154 55 0.34
155 26 0.16
156 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (150 bp):
AATAAAACTAATTTTCATTTTATAATTAGCTAGCAACATTCTTAGAAATGAAATATAATTCCGTA
TGAAATTCCGTTTCTAAGTGAAAAATTTATAGATGAAATTATTTCTGTAAATATTTCCACTCCTT
ATCTTTATAATAATCAAATA
Found at i:5739 original size:12 final size:11
Alignment explanation
Indices: 5718--5747 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
5708 TGTAGTTTCG
5718 TTTTTTTTTGT
1 TTTTTTTTTGT
5729 TTTTGTTTTTGT
1 TTTT-TTTTTGT
5741 TTTTTTT
1 TTTTTTT
5748 GTTCGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:6341 original size:13 final size:13
Alignment explanation
Indices: 6325--6354 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6315 ATAAAAAATG
6325 AAAAAAAAAGTAA
1 AAAAAAAAAGTAA
*
6338 AAAAAAAAATTAA
1 AAAAAAAAAGTAA
6351 AAAA
1 AAAA
6355 TTAAAACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (13 bp):
AAAAAAAAAGTAA
Found at i:8755 original size:16 final size:17
Alignment explanation
Indices: 8734--8770 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
8724 TTAATTTGTG
8734 GATTTTTATTAT-GTTT
1 GATTTTTATTATGGTTT
*
8750 GA-TTTTATTGTGGTTT
1 GATTTTTATTATGGTTT
8766 GATTT
1 GATTT
8771 GAACTTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 8 0.44
17 2 0.11
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.65
Consensus pattern (17 bp):
GATTTTTATTATGGTTT
Found at i:8757 original size:15 final size:16
Alignment explanation
Indices: 8737--8770 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
8727 ATTTGTGGAT
8737 TTTTATTAT-GTTTGA
1 TTTTATTATGGTTTGA
*
8752 TTTTATTGTGGTTTGA
1 TTTTATTATGGTTTGA
8768 TTT
1 TTT
8771 GAACTTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.15, C:0.00, G:0.18, T:0.68
Consensus pattern (16 bp):
TTTTATTATGGTTTGA
Found at i:9386 original size:2 final size:2
Alignment explanation
Indices: 9379--9432 Score: 90
Period size: 2 Copynumber: 26.0 Consensus size: 2
9369 ACGTTCCTTC
9379 AT AT AT AT AT AT AT AT AT AT GAT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
9422 AT AT GAT AT AT
1 AT AT -AT AT AT
9433 TACATGAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 46 0.92
3 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9409 original size:27 final size:27
Alignment explanation
Indices: 9379--9432 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
9369 ACGTTCCTTC
9379 ATATATATATATATATATATGATATAT
1 ATATATATATATATATATATGATATAT
9406 ATATATATATATATATATATGATATAT
1 ATATATATATATATATATATGATATAT
9433 TACATGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (27 bp):
ATATATATATATATATATATGATATAT
Found at i:9443 original size:13 final size:13
Alignment explanation
Indices: 9387--9443 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
9377 TCATATATAT
*
9387 ATATATATATATG
1 ATATATATACATG
* *
9400 ATATATATATATAT
1 ATATATATACAT-G
*
9414 ATATATATATATG
1 ATATATATACATG
9427 ATATAT-TACATG
1 ATATATATACATG
9439 A-ATAT
1 ATATAT
9444 TAATCTCACT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
11 4 0.10
12 6 0.15
13 18 0.45
14 12 0.30
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (13 bp):
ATATATATACATG
Done.